Description

This track was created by mapping D. mojavensis RNA-seq reads (generated by the modENCODE project) against the D. mojavensis DmojImproved assembly. The aligned RNA-seq reads are then used as input for downstream analysis using Cufflinks.

Methods

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

References

Cufflinks is a collaborative effort between the Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC Berkeley, Steven Salzberg's group at the University of Maryland Center for Bioinformatics and Computational Biology, and Barbara Wold's lab at Caltech.

The RNA-Seq data were submitted by the modENCODE project. The original RNA-Seq dataset can be obtained from the NCBI GEO database under the accession number GSE20882.